Health Data Science Sandbox

All

28 repositories

proteomics-sandbox
Public
A resource for biomedical students and researchers. Includes proteomics software tools like FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and PeptideShaker. Offers a user-friendly interface, automated identification and quantification, comprehensive data analysis, and lightweight clone feature for optimized storage.
computational-biology data-visualization data-analysis proteomics dataset-management biomedical-research proteomics-data-analysis user-friendly-interface clinical-proteomics proteomics-software
HTML
•2•9•0•0•Updated Nov 26, 2024Nov 26, 2024
GWAS_course
Public
GWAS course material
Jupyter Notebook
•0•1•0•0•Updated Nov 26, 2024Nov 26, 2024
bulk_RNAseq_course
Public
Repository for bulk RNAseq course of the Danish Health Data Science Sandbox project.
bioinformatics course ngs rnaseq-workshop bulkrnaseq
Shell
•
Creative Commons Attribution Share Alike 4.0 International
•4•6•0•0•Updated Nov 20, 2024Nov 20, 2024
R-Intro-for-HDS
Public
A short course on using R for health data science projects
HTML
•8•0•0•0•Updated Nov 15, 2024Nov 15, 2024
HPC-lab
Public
HTML
•1•0•0•0•Updated Nov 14, 2024Nov 14, 2024
hds-sandbox.github.io
Public
Website for the Health Data Science Sandbox
HTML
•2•2•0•0•Updated Nov 6, 2024Nov 6, 2024
RDM_biodata_course
Public
Short course on Research Data Management for NGS data
HTML
•
Creative Commons Attribution Share Alike 4.0 International
•2•0•0•0•Updated Nov 6, 2024Nov 6, 2024
GDKworkshops
Public
Workshops on GenomeDK cluster at Aarhus University: Introduction, pipeline creation with gwf, and more
bioinformatics pipelines high-performance-computing gwf gwf-org genomedk health-data-science-sandbox
Shell
•
Creative Commons Attribution Share Alike 4.0 International
•0•0•0•0•Updated Oct 11, 2024Oct 11, 2024
scverse-2024-workshop
Public template
Dimensionality reduction and interactive web visualization for the scverse 2024 conference
tutorial workshop projection dimensionality-reduction tsne umap laplacian scverse scverse-2024
Jupyter Notebook
•
Creative Commons Attribution Share Alike 4.0 International
•0•1•0•0•Updated Sep 16, 2024Sep 16, 2024
NGS_summer_course_Aarhus
Public
Repository for the NGS summer course at Aarhus university
Jupyter Notebook
•3•6•0•0•Updated Aug 20, 2024Aug 20, 2024
jupyterlab-quarto
Public
Quarto JupyterLab Extension which includes personalized callouts
TypeScript
•
BSD 3-Clause "New" or "Revised" License
•3•0•0•0•Updated Aug 7, 2024Aug 7, 2024
course-template
Public template
A course template for Sandbox courses
Creative Commons Attribution Share Alike 4.0 International
•2•1•0•0•Updated Jun 21, 2024Jun 21, 2024
AdvancedSingleCell
Public
Advanced tutorials for single cell data analysis
Jupyter Notebook
•
Creative Commons Attribution Share Alike 4.0 International
•0•2•0•0•Updated Jun 18, 2024Jun 18, 2024
transcriptomics_app_ucloud
Public
Development of the transcriptomics app based on Rstudio for UCloud
R
•
MIT License
•1•1•0•0•Updated Jun 11, 2024Jun 11, 2024
cc-data-template
Public
cookiecutter data template
Shell
•
MIT License
•1•0•0•0•Updated May 30, 2024May 30, 2024
PopulationGenomicsCourse
Public
Course in population genomics at BiRC
Jupyter Notebook
•7•1•0•0•Updated May 21, 2024May 21, 2024
cookiecutter-template
Public
This is a cookiecutter template for data analysis dirs by Sandbox.
Jupyter Notebook
•
Creative Commons Zero v1.0 Universal
•15•0•0•0•Updated Apr 26, 2024Apr 26, 2024
project-template
Public
This is a cookiecutter template for project folders by Sandbox.
example cookiecutter-template
Jupyter Notebook
•
Creative Commons Zero v1.0 Universal
•7•0•0•0•Updated Apr 24, 2024Apr 24, 2024
PipeItEasy
Public
Introductory workshop on implementation of pipelines with various languages (snakemake, nf-core, gwf)
Creative Commons Attribution Share Alike 4.0 International
•0•1•0•0•Updated Feb 6, 2024Feb 6, 2024
assay-template
Public
This is a cookiecutter template for NGS assay data. This template was made for a workshop at DTU in October 2023
Creative Commons Zero v1.0 Universal
•12•0•0•0•Updated Sep 22, 2023Sep 22, 2023
OMICS-workshop
Public
Introductory HDS Sandbox workshop in genomics, transcriptomics and proteomics
Creative Commons Attribution Share Alike 4.0 International
•0•1•0•0•Updated Aug 30, 2023Aug 30, 2023
AlphaFold_Workshop
Public
Predict protein folding structures using ColabFold. Gain a deeper understanding of protein folding prediction with AlphaFold2 and MMseqs2. Run the Jupyter notebook on UCloud, learn to interpret results, predict protein structures of interest. Technical requirements provided. Enhance your knowledge of protein folding and AlphaFold2's principles. Fam
bioinformatics deep-learning jupyter-notebook computational-biology ucloud protein-structure-prediction mmseqs2 alphafold colabfold protein-folding-prediction
Jupyter Notebook
•
Apache License 2.0
•0•0•0•0•Updated Aug 21, 2023Aug 21, 2023
scRNASeq_course
Public
Repository for single cell RNAseq course of the Danish Health Data Science Sandbox project.
Jupyter Notebook
•
Apache License 2.0
•2•3•2•0•Updated May 10, 2023May 10, 2023
jupyterlab_splashscreen
Public
A splash screen for jupyterlab (mutuated from ENKI lab)
TypeScript
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Mar 9, 2023Mar 9, 2023
Popgen_course_aarhus
Public
Population genomics course from AU BiRC - Prof Kasper Munch
Jupyter Notebook
•0•0•0•0•Updated Feb 16, 2023Feb 16, 2023
sdv_demo
Public
Contains demos of how to use synthetic data vault to create synthetic data
Jupyter Notebook
•1•0•0•0•Updated Feb 1, 2023Feb 1, 2023
cookiecutter-teaching
Public
Teaching template for the Health Data Science sandbox
CSS
•0•0•0•0•Updated Mar 30, 2022Mar 30, 2022
docker-cirrocumulus
Public
containerized data visualization tool for scRNAseq including analysis with jupyterlab and scanpy
GNU General Public License v3.0
•0•0•0•0•Updated Mar 14, 2022Mar 14, 2022